Package gov.nih.mipav.model.file.rawjp2

Class ImgReaderRAWSlice

java.lang.Object
jj2000.j2k.image.input.ImgReader
gov.nih.mipav.model.file.rawjp2.ImgReaderRAWSlice
All Implemented Interfaces:
jj2000.j2k.image.BlkImgDataSrc, jj2000.j2k.image.ImgData
Direct Known Subclasses:
ImgReaderRAWColorSlice
public class ImgReaderRAWSlice extends jj2000.j2k.image.input.ImgReader
This class implements the ImgData interface for reading slices of 16 bit unsigned data from a 3D RAW image file.

After being read the coefficients are level shifted by subtracting 2^(nominal bit range-1)

The TransferType (see ImgData) of this class is TYPE_INT.

NOTE: This class is not thread safe, for reasons of internal buffering.

See Also:
  • ImgData

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    private int
    blah
     
    private byte[]
    buf
    The line buffer.
    static int
    DC_OFFSET
    DC offset value used when reading image
    protected String
    fName
     
    protected ModelImage
    image
    image store
    protected RandomAccessFile
    in
    Where to read the data from
    protected jj2000.j2k.image.DataBlkInt
    intBlk
    Temporary DataBlkInt object (needed when encoder uses floating-point filters).
    private int
    offset
    The offset of the raw pixel data in the RAW file
    protected int
    rb
    The number of bits that determine the nominal dynamic range
    private boolean
    savingAsEncJP2
     
    protected boolean
    useModImg
     

    Fields inherited from class jj2000.j2k.image.input.ImgReader

    h, nc, w

  • Constructor Summary

    Constructors
    Constructor
    Description
    ImgReaderRAWSlice(ModelImage image, int si, boolean savingAsEncJP2)
     
    ImgReaderRAWSlice(ModelImage image, int si, int ti, boolean savingAsEncJP2)
     
    ImgReaderRAWSlice(File file, int si)
    Creates a new PGM file reader from the specified file.
    ImgReaderRAWSlice(RandomAccessFile in, int si)
    Creates a new PGM file reader from the specified RandomAccessFile object.
    ImgReaderRAWSlice(String fname, int si)
    Creates a new PGM file reader from the specified file name.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    close()
    Closes the underlying RandomAccessFile from where the image data is being read.
    jj2000.j2k.image.DataBlk
    getCompData(jj2000.j2k.image.DataBlk blk, int c)
    Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component.
    int
    getFixedPoint(int c)
    Returns the position of the fixed point in the specified component (i.e. the number of fractional bits), which is always 0 for this ImgReader.
    jj2000.j2k.image.DataBlk
    getInternCompData(jj2000.j2k.image.DataBlk blk, int c)
    Returns, in the blk argument, the block of image data containing the specifed rectangular area, in the specified component.
    int
    getNomRangeBits(int c)
    Returns the number of bits corresponding to the nominal range of the data in the specified component.
    boolean
    isOrigSigned(int c)
    Returns true if the data read was originally signed in the specified component, false if not.
    void
    setSliceIndex(int si, boolean useModImg)
     
    void
    setSliceIndex(int si, int ti, boolean useModImg)
     
    String
    toString()
    Returns a string of information about the object, more than 1 line long.

    Methods inherited from class jj2000.j2k.image.input.ImgReader

    getCompImgHeight, getCompImgWidth, getCompSubsX, getCompSubsY, getCompULX, getCompULY, getImgHeight, getImgULX, getImgULY, getImgWidth, getNomTileHeight, getNomTileWidth, getNumComps, getNumTiles, getNumTiles, getTile, getTileCompHeight, getTileCompWidth, getTileHeight, getTileIdx, getTilePartULX, getTilePartULY, getTileWidth, nextTile, setTile

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

  • Field Details

    • DC_OFFSET

      public static int DC_OFFSET
      DC offset value used when reading image

    • in

      protected RandomAccessFile in
      Where to read the data from

    • offset

      private int offset
      The offset of the raw pixel data in the RAW file

    • image

      protected ModelImage image
      image store

    • rb

      protected int rb
      The number of bits that determine the nominal dynamic range

    • buf

      private byte[] buf
      The line buffer.

    • intBlk

      protected jj2000.j2k.image.DataBlkInt intBlk
      Temporary DataBlkInt object (needed when encoder uses floating-point filters). This avoid allocating new DataBlk at each time

    • useModImg

      protected boolean useModImg

    • fName

      protected String fName

    • savingAsEncJP2

      private boolean savingAsEncJP2

    • blah

      private int blah

  • Constructor Details

    • ImgReaderRAWSlice

      public ImgReaderRAWSlice(File file, int si) throws IOException
      Creates a new PGM file reader from the specified file.
      Parameters:
      file - The input file.
      Throws:
      IOException - If an error occurs while opening the file.

    • ImgReaderRAWSlice

      public ImgReaderRAWSlice(String fname, int si) throws IOException
      Creates a new PGM file reader from the specified file name.
      Parameters:
      fname - The input file name.
      Throws:
      IOException - If an error occurs while opening the file.

    • ImgReaderRAWSlice

      public ImgReaderRAWSlice(RandomAccessFile in, int si) throws EOFException, IOException
      Creates a new PGM file reader from the specified RandomAccessFile object. The file header is read to acquire the image size.
      Parameters:
      in - From where to read the data
      Throws:
      EOFException - if an EOF is read
      IOException - if an error occurs when opening the file

    • ImgReaderRAWSlice

      public ImgReaderRAWSlice(ModelImage image, int si, boolean savingAsEncJP2)

    • ImgReaderRAWSlice

      public ImgReaderRAWSlice(ModelImage image, int si, int ti, boolean savingAsEncJP2)

  • Method Details

    • close

      public void close() throws IOException
      Closes the underlying RandomAccessFile from where the image data is being read. No operations are possible after a call to this method.
      Specified by:
      close in class jj2000.j2k.image.input.ImgReader
      Throws:
      IOException - If an I/O error occurs.

    • getNomRangeBits

      public int getNomRangeBits(int c)
      Returns the number of bits corresponding to the nominal range of the data in the specified component. This is the value rb (range bits) that was specified in the constructor, which normally is 8 for non bilevel data, and 1 for bilevel data.

      If this number is b then the nominal range is between -2^(b-1) and 2^(b-1)-1, since unsigned data is level shifted to have a nominal average of 0.

      Parameters:
      c - The index of the component.
      Returns:
      The number of bits corresponding to the nominal range of the data. Fro floating-point data this value is not applicable and the return value is undefined.

    • getFixedPoint

      public int getFixedPoint(int c)
      Returns the position of the fixed point in the specified component (i.e. the number of fractional bits), which is always 0 for this ImgReader.
      Parameters:
      c - The index of the component.
      Returns:
      The position of the fixed-point (i.e. the number of fractional bits). Always 0 for this ImgReader.

    • getInternCompData

      public jj2000.j2k.image.DataBlk getInternCompData(jj2000.j2k.image.DataBlk blk, int c)
      Returns, in the blk argument, the block of image data containing the specifed rectangular area, in the specified component. The data is returned, as a reference to the internal data, if any, instead of as a copy, therefore the returned data should not be modified.

      After being read the coefficients are level shifted by subtracting 2^(nominal bit range - 1)

      The rectangular area to return is specified by the 'ulx', 'uly', 'w' and 'h' members of the 'blk' argument, relative to the current tile. These members are not modified by this method. The 'offset' and 'scanw' of the returned data can be arbitrary. See the 'DataBlk' class.

      If the data array in blk is null, then a new one is created if necessary. The implementation of this interface may choose to return the same array or a new one, depending on what is more efficient. Therefore, the data array in blk prior to the method call should not be considered to contain the returned data, a new array may have been created. Instead, get the array from blk after the method has returned.

      The returned data always has its 'progressive' attribute unset (i.e. false).

      When an I/O exception is encountered the JJ2KExceptionHandler is used. The exception is passed to its handleException method. The action that is taken depends on the action that has been registered in JJ2KExceptionHandler. See JJ2KExceptionHandler for details.

      Parameters:
      blk - Its coordinates and dimensions specify the area to return. Some fields in this object are modified to return the data.
      c - The index of the component from which to get the data. Only 0 is valid.
      Returns:
      The requested DataBlk
      See Also:

    • getCompData

      public jj2000.j2k.image.DataBlk getCompData(jj2000.j2k.image.DataBlk blk, int c)
      Returns, in the blk argument, a block of image data containing the specifed rectangular area, in the specified component. The data is returned, as a copy of the internal data, therefore the returned data can be modified "in place".

      After being read the coefficients are level shifted by subtracting 2^(nominal bit range - 1)

      The rectangular area to return is specified by the 'ulx', 'uly', 'w' and 'h' members of the 'blk' argument, relative to the current tile. These members are not modified by this method. The 'offset' of the returned data is 0, and the 'scanw' is the same as the block's width. See the 'DataBlk' class.

      If the data array in 'blk' is 'null', then a new one is created. If the data array is not 'null' then it is reused, and it must be large enough to contain the block's data. Otherwise an 'ArrayStoreException' or an 'IndexOutOfBoundsException' is thrown by the Java system.

      The returned data has its 'progressive' attribute unset (i.e. false).

      This method just calls 'getInternCompData(blk, n)'.

      When an I/O exception is encountered the JJ2KExceptionHandler is used. The exception is passed to its handleException method. The action that is taken depends on the action that has been registered in JJ2KExceptionHandler. See JJ2KExceptionHandler for details.

      Parameters:
      blk - Its coordinates and dimensions specify the area to return. If it contains a non-null data array, then it must have the correct dimensions. If it contains a null data array a new one is created. The fields in this object are modified to return the data.
      c - The index of the component from which to get the data. Only 0 is valid.
      Returns:
      The requested DataBlk
      See Also:

    • setSliceIndex

      public void setSliceIndex(int si, boolean useModImg) throws IOException
      Throws:
      IOException

    • setSliceIndex

      public void setSliceIndex(int si, int ti, boolean useModImg) throws IOException
      Throws:
      IOException

    • isOrigSigned

      public boolean isOrigSigned(int c)
      Returns true if the data read was originally signed in the specified component, false if not. This method returns always false since PGM data is always unsigned.
      Specified by:
      isOrigSigned in class jj2000.j2k.image.input.ImgReader
      Parameters:
      c - The index of the component, from 0 to N-1.
      Returns:
      always false, since PGM data is always unsigned.

    • toString

      public String toString()
      Returns a string of information about the object, more than 1 line long. The information string includes information from the underlying RandomAccessIO (its toString() method is called in turn).
      Overrides:
      toString in class Object
      Returns:
      A string of information about the object.